Related papers: Oxidative stress response: a proteomic view
For the outcomes and phenotypes of complex diseases, multiple types of molecular (genetic, genomic, epigenetic, etc.) changes, environmental risk factors, and their interactions have been found to have important contributions. In each of…
The shape of a polymer plays an important role in determining its interactions with other molecules and with the environment, and is in turn affected by both of them. As a consequence, in the literature the shape properties of a chain in…
Our recent modelling works and corresponding numerical simulations realized to describe the UO2 oxidation processes confirm the theory showing that an applied mechanical strain can strongly affect the local oxygen diffusion in a stressed…
Biochemical reaction networks are subjected to large fluctuations attributable to small molecule numbers, yet underlie reliable biological functions. Most theoretical approaches describe them as purely deterministic or stochastic dynamical…
In this paper, attention is drawn to the importance of accounting for osmotic pressure when analyzing physiological effects on cellular structures in plasma medicine. Interaction of a weakly ionized plasma jet with a saline solution leads…
In this paper we develop a model of stochastic gene expression, which is an extension of the model investigated in the paper [T. Lipniacki, P. Paszek, A. Marciniak-Czochra, A.R. Brasier, M. Kimmel, Transcriptional stochasticity in gene…
Diffusion-mediated surface phenomena are crucial for human life and industry, with examples ranging from oxygen capture by lung alveolar surface to heterogeneous catalysis, gene regulation, membrane permeation and filtration processes.…
Tuning of active prestress e.g. through activity of molecular motors constitutes a powerful cellular tool to adjust cellular stiffness through nonlinear material properties. Understanding this tool is an important prerequisite for our…
The concept of allostery in which macromolecules switch between two different conformations is a central theme in biological processes ranging from gene regulation to cell signaling to enzymology. Allosteric enzymes pervade metabolic…
Allosteric regulation is often viewed as thermodynamic in nature. However protein internal motions during an enzymatic reaction cycle can be slow hopping processes over numerous potential barriers. We propose that regulating molecules may…
The paper gives an account of a detailed investigation of the thermodynamic branch as a path of the chemical system deviation from its isolated thermodynamic equilibrium under an external impact. For a combination of direct and reverse…
We investigate the potential of numerical algorithms to decipher the kinetic parameters involved in multi-step chemical reactions. To this end we study a dimerization kinetics of protein as a model system. We follow the dimerization…
Pressure provides a powerful parameter to control the protein conformation state, which at sufficiently high values can lead to unfolding. Here, we investigate the effects of increasing pressure up to $0.4$ GPa on hydrated lysozyme…
In the theoretical modelling of a physical system a crucial step consists in the identification of those degrees of freedom that enable a synthetic, yet informative representation of it. While in some cases this selection can be carried out…
Bioprinting is an enabling biofabrication technique to create heterogeneous tissue constructs according to patient-specific geometries and compositions. Optimization of bioinks as per requirements for specific tissue applications is a…
In this paper, we present a probabilistic analysis of a dynamical particle model for the self-adaptive immune response to cancer, as proposed by the first author in a previous work. The model is motivated by the interplay between immune…
Self-assembly of protein monomers into distinct membrane protein oligomers provides a general mechanism for diversity in the molecular architectures, and resulting biological functions, of membrane proteins. We develop a general physical…
Biological organisms are composed of numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted. Thus, understanding these biochemical processes and their interrelationships is a…
Cooperativity plays an important role in the action of proteins bound to DNA. A simple, mechanical mechanism for cooperativity, in the form of a tension-mediated interaction between proteins bound to DNA at two different locations is…
Motivation: Protein interactions are fundamental building blocks of biochemical reaction systems underlying cellular functions. The complexity and functionality of such systems emerge not from the protein interactions themselves but from…